Package: CRBHits
Title: Conditional reciprocal best hits (CRBHits) in R
Version: 0.0.10
Authors@R: 
    person(given = "Kristian K",
           family = "Ullrich",
           role = c("aut", "cre"),
           email = "ullrich@evolbio.mpg.de",
           comment = c(ORCID = "0000-0003-4308-9626"))
Description: CRBHits calculates conditional reciprocal best hit
        (CRBHit) pairs and subsequently can classify tandem duplicates,
        assign syntney groups and calculate Ka/Ks values.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.5.0)
Imports: Biostrings, MSA2dist (>= 1.12.0), curl, doParallel, dplyr,
        foreach, ggplot2, graphics, gridExtra, grDevices, methods,
        parallel, readr, rlang, stats, stringr, tidyr, utils
Suggests: ape, rmarkdown, knitr, devtools, seqinr, stringi, testthat,
        tibble
VignetteBuilder: knitr
biocViews: Software, Alignment, Genetics
NeedsCompilation: yes
SystemRequirements: LAST (https://anaconda.org/bioconda/last),
        DAGchainer (https://anaconda.org/bioconda/dagchainer), DIAMOND
        (optional, https://anaconda.org/bioconda/diamond), MMSEQS2
        (optiona, https://anaconda.org/bioconda/mmseqs2), LAMBDA
        (optional, https://anaconda.org/bioconda/lambda), GNU make,
        libcurl (deb: libcurl4-openssl-dev or CentOS: libcurl-devel),
        openssl (deb: libssl-dev or CentOS: openssl-devel), libxml2
        (deb: libxml2-dev or CentOS: libxml2-devel), libGLU (deb:
        libglu1-mesa-dev or CentOS: mesa-libGLU-devel), libgit2-devel
        (deb: libgit2-dev or CentOS: libgit2-devel)
URL: https://github.com/kullrich/CRBHits,
        https://kullrich.github.io/CRBHits/
BugReports: https://github.com/kullrich/CRBHits/issues
RoxygenNote: 7.3.2
Config/pak/sysreqs: make libgit2-dev libicu-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://kullrich.r-universe.dev
Date/Publication: 2025-05-21 16:54:01 UTC
RemoteUrl: https://github.com/kullrich/crbhits
RemoteRef: HEAD
RemoteSha: 158ea52a96bbcb0928e384ac15015597aaa987bc
Packaged: 2026-07-10 07:13:07 UTC; root
Author: Kristian K Ullrich [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4308-9626>)
Maintainer: Kristian K Ullrich <ullrich@evolbio.mpg.de>